This module provides strong suggestions for any intended HSP tilingobject implementation. An object subclassing TilingI should overridethe methods defined here according to their descriptions below.See the section STATISTICS METHODS for hints on implementing methodsthat are valid across different algorithms and report types.

Title : length Usage : $max_length = $tiling->length($type) Function: Return the total number of residues of the subject or query sequence covered by the tiling Returns : number of "logical" residues covered Args : scalar $type, one of 'hit', 'subject', 'query'

Please direct usage questions or support issues to the mailing list:bioperl-l@bioperl.orgrather than to the module maintainer directly. Many experienced andreponsive experts will be able look at the problem and quicklyaddress it. Please include a thorough description of the problemwith code and data examples if at all possible.

The tiling statistics can be thought of as global counterparts tosimilar statistics defined for the individual HSPs. We thereforeprescribe definitions for many of the synonymous methods defined inBio::Search::HSP::HSPI.The tiling statistics must be able to keep track of the coordinatesystems in which both the query and subject sequences exist; i.e.,either nucleotide or amino acid. This information is typicallyinferred from the name of the algorithm used to perform the originalsearch (contained in $hit_object-E<gt>algorithm). Here is a tableof algorithm information that may be useful (if you trust us).

Statistics methods must also be aware of differences in reportingamong the algorithms. Hit attributes are not necessarily normalizedover all algorithms. Devs, please feel free to add examples to thelist below.

NCBI BLAST vs WU-BLAST (AB-BLAST) lengths

The total length of the alignment is reported differently between these two flavors. $hit_object-E<gt>length() will contain the number in the denominator of the stats line; i.e., 120 in

Identical = 34/120 Positives = 67/120

NCBI BLAST uses the total length of the query sequence as input by the user (a.k.a. "with gaps"). WU-BLAST uses the length of the query sequence actually aligned by the algorithm (a.k.a. "without gaps").Finally, developers should remember that sequence data may or may notbe associated with the HSPs contained in the hit object. This willtypically depend on whether a full report (e.g, blastall -m0) or asummary (e.g., blastall -m8) was parsed. Statistics methods thatdepend directly on the sequence data will need to check thatthat data is present.